noone@mail.com Analysis of Dieting study 16S data % Fri Sep 7 05:46:18 2018

(1.6.1.4) Taxonomic level: otu of Subset: Patient samples

(1.6.1.4.1) Loading counts and metadata

Subreport

(1.6.1.4.2) Data analysis
(1.6.1.4.2.1) Richness and diversity estimates Before count filtering

Subreport

Filtering abundance matrix with arguments [ min_mean :10, min_quant_incidence_frac:0.25, min_quant_mean_frac :0.25]. Filtering features

Note that some community richness estimators will not work correctly if provided with abundance-filtered counts

After filtering, left 67 records for 113 features

Wrote counts and metadata for raw counts After final feature filtering to files data/1.6.1.4.2.1-3233b4c0ccdsamples.raw.16s.l.otu.count.tsv,data/1.6.1.4.2.1-3233b4c0ccdsamples.raw.16s.l.otu.attr.tsv

Wrote counts and metadata for proportions counts After final feature filtering to files data/1.6.1.4.2.1-32320999416samples.proportions.16s.l.otu.count.tsv,data/1.6.1.4.2.1-32320999416samples.proportions.16s.l.otu.attr.tsv

(1.6.1.4.2.2) DESeq2 tests and data normalization

Love MI, Huber W, Anders S (2014). “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.” Genome Biology, 15, 550. doi: 10.1186/s13059-014-0550-8 (URL: http://doi.org/10.1186/s13059-014-0550-8).

(1.6.1.4.2.2.1) Table 445. DESeq2 results for task: visit;[ alpha:0.05]. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.6.1.4.2.2.1-323604c7d0a.1.6.1.4.2.2.1.a.nam.csv

feature baseMean log2FoldChange lfcSE stat pvalue padj i.baseMean baseVar allZero dispGeneEst dispGeneIter dispFit dispersion dispIter dispOutlier dispMAP Intercept visit SE_Intercept SE_visit WaldStatistic_Intercept WaldStatistic_visit WaldPvalue_Intercept WaldPvalue_visit betaConv betaIter deviance maxCooks replace
Enterococcus.Otu1019 22.0542 -2.908762 0.6374 -4.563208 5.038e-06 0.0005592 22.0542 2.748e+04 FALSE 16.191 14 8.239 15.503 8 FALSE 15.503 8.6262 -2.908762 1.5740 0.6374 5.4805 -4.563208 4.241e-08 5.038e-06 TRUE 100 186.60 NA TRUE
Prevotella.Otu1987 79.1924 -3.042806 0.7501 -4.056722 4.977e-05 0.0027620 79.1924 1.007e+05 FALSE 23.878 8 7.919 22.477 9 FALSE 22.477 12.1590 -3.042806 1.8783 0.7501 6.4735 -4.056722 9.577e-11 4.977e-05 TRUE 100 249.41 NA TRUE
Haemophilus.Otu1497 15.4553 1.475114 0.3938 3.745766 1.798e-04 0.0066542 15.4553 4.992e+03 FALSE 5.883 13 9.151 5.977 11 FALSE 5.977 -0.2464 1.475114 1.0096 0.3938 -0.2440 3.745766 8.072e-01 1.798e-04 TRUE 19 335.22 NA TRUE
Clostridiaceae_1.Otu1955 10.0364 1.629175 0.4537 3.590963 3.295e-04 0.0091425 10.0364 1.435e+03 FALSE 7.738 11 12.386 7.893 11 FALSE 7.893 -1.0547 1.629175 1.1653 0.4537 -0.9051 3.590963 3.654e-01 3.295e-04 TRUE 28 280.04 NA FALSE
Lachnospiraceae.Otu0033 12.5077 1.767830 0.5379 3.286778 1.013e-03 0.0224976 12.5077 2.660e+03 FALSE 11.274 9 10.475 11.231 6 FALSE 11.231 -1.4113 1.767830 1.3762 0.5379 -1.0255 3.286778 3.051e-01 1.013e-03 TRUE 28 244.44 NA TRUE
Lachnospiraceae.Otu2222 40.1708 1.188295 0.3917 3.033747 2.415e-03 0.0398258 40.1708 1.666e+04 FALSE 6.048 11 11.136 6.161 10 FALSE 6.161 2.1842 1.188295 0.9907 0.3917 2.2047 3.033747 2.748e-02 2.415e-03 TRUE 19 457.56 NA FALSE
Prevotella.Otu2602 10.8772 -3.047929 1.0086 -3.021948 2.512e-03 0.0398258 10.8772 1.961e+03 FALSE 48.054 9 11.580 40.347 8 FALSE 40.347 8.9647 -3.047929 2.5201 1.0086 3.5572 -3.021948 3.748e-04 2.512e-03 TRUE 100 135.55 NA TRUE
Lachnospiracea_incertae_sedis.Otu0113 24.3699 0.802529 0.2787 2.879989 3.977e-03 0.0451315 24.3699 3.294e+03 FALSE 2.986 12 9.174 3.074 8 FALSE 3.074 2.5825 0.802529 0.7074 0.2787 3.6507 2.879989 2.615e-04 3.977e-03 TRUE 10 501.17 NA FALSE
Lachnospiracea_incertae_sedis.Otu0778 70.9469 1.058229 0.3694 2.864425 4.178e-03 0.0451315 70.9469 3.639e+04 FALSE 5.456 12 7.955 5.511 7 FALSE 5.511 3.2900 1.058229 0.9327 0.3694 3.5273 2.864425 4.198e-04 4.178e-03 TRUE 19 526.87 NA FALSE
Akkermansia.Otu1935 5.4333 -2.290062 0.8059 -2.841560 4.489e-03 0.0451315 5.4333 1.051e+03 FALSE 26.303 9 18.635 25.305 7 FALSE 25.305 5.9242 -2.290062 2.0064 0.8059 2.9526 -2.841560 3.151e-03 4.489e-03 TRUE 14 122.38 NA TRUE
Prevotella.Otu0634 6.6784 -1.964089 0.6914 -2.840674 4.502e-03 0.0451315 6.6784 8.469e+02 FALSE 18.542 10 17.401 18.452 7 FALSE 18.452 5.8660 -1.964089 1.7165 0.6914 3.4175 -2.840674 6.321e-04 4.502e-03 TRUE 100 163.22 NA TRUE
Prevotella.Otu2501 8.6603 -2.569447 0.9128 -2.814910 4.879e-03 0.0451315 8.6603 1.832e+03 FALSE 36.628 9 14.227 32.837 8 FALSE 32.837 7.3518 -2.569447 2.2774 0.9128 3.2282 -2.814910 1.246e-03 4.879e-03 TRUE 100 140.91 NA TRUE
Roseburia.Otu2084 26.5790 0.642684 0.2402 2.675117 7.470e-03 0.0637850 26.5790 1.995e+03 FALSE 2.186 9 10.435 2.278 10 FALSE 2.278 3.0845 0.642684 0.6100 0.2402 5.0566 2.675117 4.268e-07 7.470e-03 TRUE 7 539.31 NA FALSE
Prevotella.Otu1633 17.0646 -1.544686 0.6031 -2.561229 1.043e-02 0.0767979 17.0646 5.629e+03 FALSE 14.883 8 8.597 14.445 9 FALSE 14.445 6.5823 -1.544686 1.5093 0.6031 4.3611 -2.561229 1.294e-05 1.043e-02 TRUE 100 231.55 NA TRUE
Bacteroides.Otu2654 134.4818 -0.894052 0.3541 -2.524975 1.157e-02 0.0767979 134.4818 2.077e+05 FALSE 5.030 13 8.095 5.084 9 FALSE 5.084 8.6875 -0.894052 0.8913 0.3541 9.7468 -2.524975 1.903e-22 1.157e-02 TRUE 18 609.54 NA TRUE
Bacteroides.Otu2625 31.9661 -1.066211 0.4228 -2.521841 1.167e-02 0.0767979 31.9661 8.831e+03 FALSE 7.053 13 12.754 7.190 11 FALSE 7.190 6.9866 -1.066211 1.0625 0.4228 6.5758 -2.521841 4.839e-11 1.167e-02 TRUE 23 411.21 NA TRUE
Prevotella.Otu1319 6.6243 -2.729223 1.0834 -2.519210 1.176e-02 0.0767979 6.6243 9.934e+02 FALSE 54.949 11 17.468 46.690 9 FALSE 46.690 7.7593 -2.729223 2.7101 1.0834 2.8631 -2.519210 4.195e-03 1.176e-02 TRUE 100 115.92 NA TRUE
Alistipes.Otu1466 52.5129 -1.220111 0.4975 -2.452539 1.419e-02 0.0874755 52.5129 1.652e+04 FALSE 10.075 10 8.574 10.005 9 FALSE 10.005 7.8831 -1.220111 1.2512 0.4975 6.3005 -2.452539 2.967e-10 1.419e-02 TRUE 100 416.69 NA TRUE
Lachnospiraceae.Otu2076 10.8021 0.989917 0.4096 2.416981 1.565e-02 0.0879799 10.8021 3.826e+02 FALSE 6.418 8 11.645 6.586 11 FALSE 6.586 0.8406 0.989917 1.0428 0.4096 0.8061 2.416981 4.202e-01 1.565e-02 TRUE 13 345.84 NA FALSE
Roseburia.Otu1051 35.9214 0.586603 0.2432 2.412300 1.585e-02 0.0879799 35.9214 3.625e+03 FALSE 2.268 12 12.369 2.356 12 FALSE 2.356 3.6703 0.586603 0.6158 0.2432 5.9602 2.412300 2.519e-09 1.585e-02 TRUE 7 572.96 NA FALSE
Parabacteroides.Otu1736 99.0931 -1.178877 0.4944 -2.384646 1.710e-02 0.0903623 99.0931 2.126e+05 FALSE 9.983 13 7.996 9.914 9 FALSE 9.914 8.8386 -1.178877 1.2443 0.4944 7.1034 -2.384646 1.217e-12 1.710e-02 TRUE 100 449.22 NA TRUE
Lachnospiraceae.Otu2512 15.4602 0.792931 0.3424 2.316028 2.056e-02 0.0991528 15.4602 1.318e+03 FALSE 4.542 11 9.149 4.638 10 FALSE 4.638 1.9753 0.792931 0.8692 0.3424 2.2725 2.316028 2.305e-02 2.056e-02 TRUE 14 409.15 NA TRUE
Bacteroides.Otu1201 41.4326 -0.789022 0.3431 -2.299456 2.148e-02 0.0991528 41.4326 4.993e+03 FALSE 4.630 10 10.750 4.743 8 FALSE 4.743 6.8919 -0.789022 0.8631 0.3431 7.9850 -2.299456 1.405e-15 2.148e-02 TRUE 20 519.61 NA TRUE
Roseburia.Otu2728 6.8498 0.791934 0.3462 2.287355 2.218e-02 0.0991528 6.8498 1.791e+02 FALSE 4.356 12 17.180 4.584 11 FALSE 4.584 0.7743 0.791934 0.8873 0.3462 0.8726 2.287355 3.829e-01 2.218e-02 TRUE 10 331.68 NA TRUE
Turicibacter.Otu0468 4.0189 -1.090992 0.4796 -2.274925 2.291e-02 0.0991528 4.0189 1.946e+02 FALSE 8.303 12 19.894 8.711 8 FALSE 8.711 4.0133 -1.090992 1.1916 0.4796 3.3681 -2.274925 7.568e-04 2.291e-02 TRUE 10 218.20 NA TRUE
Gemmiger.Otu0907 8.8437 -0.854112 0.3763 -2.269713 2.322e-02 0.0991528 8.8437 3.226e+02 FALSE 5.329 12 13.934 5.532 11 FALSE 5.532 4.7958 -0.854112 0.9423 0.3763 5.0897 -2.269713 3.587e-07 2.322e-02 TRUE 11 338.46 NA TRUE
Bacteroides.Otu2460 16.1069 -0.732744 0.3285 -2.230903 2.569e-02 0.1056043 16.1069 1.345e+03 FALSE 4.184 9 8.905 4.277 11 FALSE 4.277 5.4493 -0.732744 0.8248 0.3285 6.6066 -2.230903 3.933e-11 2.569e-02 TRUE 10 418.26 NA FALSE
Bacteroidales.Otu0696 4.1520 -2.075671 0.9502 -2.184503 2.893e-02 0.1146682 4.1520 9.081e+02 FALSE 38.618 10 19.713 35.749 7 FALSE 35.749 6.3429 -2.075671 2.3747 0.9502 2.6711 -2.184503 7.561e-03 2.893e-02 TRUE 27 108.63 NA TRUE
Prevotella.Otu1803 6.7924 -2.155166 1.0187 -2.115614 3.438e-02 0.1286206 6.7924 9.353e+02 FALSE 46.811 6 17.255 41.284 8 FALSE 41.284 6.8484 -2.155166 2.5488 1.0187 2.6869 -2.115614 7.212e-03 3.438e-02 TRUE 100 125.13 NA TRUE
Bacteroides.Otu0863 150.0905 -0.789292 0.3739 -2.111116 3.476e-02 0.1286206 150.0905 1.551e+05 FALSE 5.625 9 8.093 5.674 8 FALSE 5.674 8.7230 -0.789292 0.9413 0.3739 9.2665 -2.111116 1.923e-20 3.476e-02 TRUE 28 616.18 NA FALSE
Roseburia.Otu2637 10.3061 0.688995 0.3383 2.036558 4.169e-02 0.1467411 10.3061 4.150e+02 FALSE 4.315 15 12.106 4.470 10 FALSE 4.470 1.5942 0.688995 0.8616 0.3383 1.8502 2.036558 6.428e-02 4.169e-02 TRUE 9 374.77 NA FALSE
Bacteroides.Otu2523 3.1040 -1.274168 0.6275 -2.030520 4.230e-02 0.1467411 3.1040 1.742e+02 FALSE 14.487 12 22.528 15.016 10 FALSE 15.016 3.7061 -1.274168 1.5603 0.6275 2.3753 -2.030520 1.753e-02 4.230e-02 TRUE 27 148.33 NA TRUE
Lachnospiraceae.Otu0898 25.1065 0.566271 0.2808 2.016877 4.371e-02 0.1470190 25.1065 4.468e+03 FALSE 3.054 13 9.574 3.140 9 FALSE 3.140 3.2733 0.566271 0.7110 0.2808 4.6040 2.016877 4.145e-06 4.371e-02 TRUE 12 509.25 NA FALSE
Lachnospiraceae.Otu0491 11.0955 0.678930 0.3531 1.922806 5.450e-02 0.1779409 11.0955 1.063e+03 FALSE 4.775 14 11.401 4.910 11 FALSE 4.910 1.8234 0.678930 0.8972 0.3531 2.0324 1.922806 4.211e-02 5.450e-02 TRUE 16 373.13 NA FALSE
Bacteroides.Otu2416 16.9176 -0.597893 0.3292 -1.816258 6.933e-02 0.2197858 16.9176 1.942e+03 FALSE 4.222 10 8.640 4.314 10 FALSE 4.314 5.2947 -0.597893 0.8278 0.3292 6.3964 -1.816258 1.591e-10 6.933e-02 TRUE 11 433.18 NA FALSE
Prevotella.Otu0882 5.6152 -1.632220 0.9111 -1.791515 7.321e-02 0.2197858 5.6152 3.680e+02 FALSE 35.527 9 18.491 32.901 7 FALSE 32.901 5.3042 -1.632220 2.2791 0.9111 2.3274 -1.791515 1.995e-02 7.321e-02 TRUE 23 138.69 NA TRUE
Prevotella.Otu1994 4.8509 -2.318720 1.2945 -1.791196 7.326e-02 0.2197858 4.8509 1.022e+03 FALSE 67.000 8 19.064 67.000 4 FALSE 67.000 5.4783 -2.318720 3.2461 1.2945 1.6877 -1.791196 9.148e-02 7.326e-02 TRUE 25 63.60 NA TRUE
Lachnospiracea_incertae_sedis.Otu0651 29.2886 0.654808 0.3711 1.764366 7.767e-02 0.2268791 29.2886 5.076e+03 FALSE 5.424 9 11.923 5.543 9 FALSE 5.543 3.2886 0.654808 0.9375 0.3711 3.5077 1.764366 4.520e-04 7.767e-02 TRUE 19 454.18 NA FALSE
Bacteroides.Otu2120 26.9710 -0.704644 0.4062 -1.734618 8.281e-02 0.2356858 26.9710 4.899e+03 FALSE 6.545 11 10.668 6.652 11 FALSE 6.652 6.2225 -0.704644 1.0221 0.4062 6.0880 -1.734618 1.144e-09 8.281e-02 TRUE 20 435.96 NA FALSE
Veillonella.Otu0362 5.1406 0.643776 0.3853 1.670800 9.476e-02 0.2629622 5.1406 2.803e+02 FALSE 5.437 13 18.852 5.698 11 FALSE 5.698 0.7683 0.643776 0.9853 0.3853 0.7797 1.670800 4.356e-01 9.476e-02 TRUE 14 278.20 NA TRUE
Bacteroides.Otu0929 157.2333 -0.593916 0.3607 -1.646460 9.967e-02 0.2645967 157.2333 1.321e+05 FALSE 5.227 11 8.094 5.284 8 FALSE 5.284 8.4925 -0.593916 0.9084 0.3607 9.3490 -1.646460 8.848e-21 9.967e-02 TRUE 17 657.35 NA FALSE
Bacteroides.Otu2520 346.7264 -0.591560 0.3598 -1.644283 1.001e-01 0.2645967 346.7264 4.893e+05 FALSE 5.223 9 7.294 5.262 10 FALSE 5.262 9.6202 -0.591560 0.9060 0.3598 10.6177 -1.644283 2.465e-26 1.001e-01 TRUE 29 734.07 NA TRUE
Bacteroides.Otu0661 108.5792 -0.566975 0.3640 -1.557480 1.194e-01 0.3038717 108.5792 5.813e+04 FALSE 5.321 15 8.046 5.377 8 FALSE 5.377 7.9163 -0.566975 0.9167 0.3640 8.6357 -1.557480 5.835e-18 1.194e-01 TRUE 17 615.75 NA FALSE
Alistipes.Otu2508 44.5275 -0.796011 0.5151 -1.545429 1.222e-01 0.3038717 44.5275 9.480e+03 FALSE 10.783 9 9.885 10.751 8 FALSE 10.751 7.0440 -0.796011 1.2966 0.5151 5.4328 -1.545429 5.548e-08 1.222e-01 TRUE 100 403.53 NA TRUE
Bacteroides.Otu0480 12.7779 -1.247392 0.8139 -1.532680 1.254e-01 0.3038717 12.7779 2.787e+03 FALSE 28.958 7 10.336 26.722 10 FALSE 26.722 6.1521 -1.247392 2.0458 0.8139 3.0072 -1.532680 2.637e-03 1.254e-01 TRUE 25 174.32 NA TRUE
Bacteroides.Otu0069 95.3446 -0.454045 0.2977 -1.525409 1.272e-01 0.3038717 95.3446 2.359e+04 FALSE 3.520 12 7.976 3.589 9 FALSE 3.589 7.5243 -0.454045 0.7496 0.2977 10.0380 -1.525409 1.037e-23 1.272e-01 TRUE 12 667.53 NA FALSE
Bacteroides.Otu0877 23.1949 -0.484839 0.3191 -1.519382 1.287e-01 0.3038717 23.1949 2.279e+03 FALSE 3.995 10 8.623 4.078 10 FALSE 4.078 5.5213 -0.484839 0.8032 0.3191 6.8741 -1.519382 6.238e-12 1.287e-01 TRUE 11 471.53 NA TRUE
Blautia.Otu0620 7.7847 -0.385088 0.2599 -1.481560 1.385e-01 0.3141281 7.7847 2.933e+02 FALSE 2.429 14 15.761 2.572 10 FALSE 2.572 3.7884 -0.385088 0.6544 0.2599 5.7891 -1.481560 7.076e-09 1.385e-01 TRUE 9 394.65 NA TRUE
Klebsiella.Otu1452 1.0116 0.812096 0.5484 1.480765 1.387e-01 0.3141281 1.0116 8.690e+00 FALSE 10.003 10 28.015 11.138 6 FALSE 11.138 -2.2459 0.812096 1.4079 0.5484 -1.5952 1.480765 1.107e-01 1.387e-01 TRUE 12 129.11 NA TRUE
Clostridiales.Otu0562 2.3282 1.396214 0.9851 1.417322 1.564e-01 0.3471831 2.3282 2.307e+02 FALSE 41.623 8 25.479 38.555 9 FALSE 38.555 -2.8529 1.396214 2.4995 0.9851 -1.1414 1.417322 2.537e-01 1.564e-01 TRUE 16 92.48 NA TRUE
Prevotella.Otu2227 2.1604 -1.546603 1.1056 -1.398861 1.619e-01 0.3522720 2.1604 9.597e+01 FALSE 55.463 7 26.026 48.615 9 FALSE 48.615 4.1120 -1.546603 2.7708 1.1056 1.4840 -1.398861 1.378e-01 1.619e-01 TRUE 19 96.15 NA TRUE
Prevotella.Otu0738 1.7692 -1.358632 0.9815 -1.384296 1.663e-01 0.3549176 1.7692 1.005e+02 FALSE 40.757 8 27.078 37.993 7 FALSE 37.993 3.3392 -1.358632 2.4580 0.9815 1.3585 -1.384296 1.743e-01 1.663e-01 TRUE 15 96.45 NA TRUE
Clostridium_XlVa.Otu0236 22.3760 -0.273533 0.2087 -1.310487 1.900e-01 0.3906213 22.3760 1.247e+03 FALSE 1.647 10 8.329 1.712 10 FALSE 1.712 5.0684 -0.273533 0.5263 0.2087 9.6309 -1.310487 5.921e-22 1.900e-01 TRUE 7 543.09 NA FALSE
Barnesiella.Otu2015 1.2340 1.126669 0.8597 1.310485 1.900e-01 0.3906213 1.2340 6.374e+01 FALSE 29.180 7 27.865 29.012 6 FALSE 29.012 -2.9170 1.126669 2.1850 0.8597 -1.3351 1.310485 1.819e-01 1.900e-01 TRUE 15 84.04 NA TRUE
Bacteroides.Otu0848 229.7448 0.429964 0.3349 1.283810 1.992e-01 0.3972672 229.7448 3.183e+05 FALSE 4.503 12 7.997 4.557 12 FALSE 4.557 6.8028 0.429964 0.8438 0.3349 8.0621 1.283810 7.499e-16 1.992e-01 TRUE 27 721.66 NA FALSE
Prevotella.Otu2327 1.5068 -1.282004 1.0035 -1.277522 2.014e-01 0.3972672 1.5068 8.379e+01 FALSE 42.620 9 27.563 39.828 9 FALSE 39.828 3.3103 -1.282004 2.5146 1.0035 1.3165 -1.277522 1.880e-01 2.014e-01 TRUE 22 94.44 NA TRUE
Bacteroides.Otu1352 7.0324 -0.371933 0.2928 -1.270232 2.040e-01 0.3972672 7.0324 1.411e+02 FALSE 3.098 14 16.930 3.292 13 FALSE 3.292 3.6037 -0.371933 0.7374 0.2928 4.8870 -1.270232 1.024e-06 2.040e-01 TRUE 9 371.56 NA TRUE
Burkholderiales.Otu0023 1.1249 -1.613477 1.2972 -1.243817 2.136e-01 0.4068259 1.1249 8.478e+01 FALSE 67.000 2 27.942 67.000 8 FALSE 67.000 2.7978 -1.613477 3.2579 1.2972 0.8588 -1.243817 3.905e-01 2.136e-01 TRUE 14 22.42 NA TRUE
Sutterella.Otu1997 1.0856 -1.604165 1.2973 -1.236586 2.162e-01 0.4068259 1.0856 2.862e+01 FALSE 67.000 10 27.966 67.000 11 FALSE 67.000 2.7656 -1.604165 3.2581 1.2973 0.8488 -1.236586 3.960e-01 2.162e-01 TRUE 12 50.42 NA TRUE
Dorea.Otu1142 20.5783 -0.328646 0.2778 -1.182970 2.368e-01 0.4381186 20.5783 2.363e+03 FALSE 3.002 12 8.072 3.073 9 FALSE 3.073 5.0535 -0.328646 0.6999 0.2778 7.2204 -1.182970 5.185e-13 2.368e-01 TRUE 9 487.37 NA FALSE
Prevotella.Otu0773 0.7620 -1.273963 1.1084 -1.149362 2.504e-01 0.4556580 0.7620 2.096e+01 FALSE 56.340 10 28.373 48.457 8 FALSE 48.457 2.1216 -1.273963 2.7825 1.1084 0.7625 -1.149362 4.458e-01 2.504e-01 TRUE 12 67.67 NA TRUE
Phascolarctobacterium.Otu1814 5.6682 -0.670968 0.6296 -1.065638 2.866e-01 0.5033052 5.6682 3.369e+02 FALSE 15.650 14 18.447 15.823 9 FALSE 15.823 3.8167 -0.670968 1.5829 0.6296 2.4112 -1.065638 1.590e-02 2.866e-01 TRUE 14 207.44 NA TRUE
Bacteroides.Otu0001 826.4538 -0.337704 0.3213 -1.051155 2.932e-01 0.5033052 826.4538 2.010e+06 FALSE 4.191 12 4.524 4.198 8 FALSE 4.198 10.4081 -0.337704 0.8091 0.3213 12.8630 -1.051155 7.272e-38 2.932e-01 TRUE 18 915.92 NA FALSE
Clostridium_XI.Otu2681 7.5155 0.362586 0.3470 1.044925 2.961e-01 0.5033052 7.5155 2.656e+02 FALSE 4.484 11 16.203 4.696 12 FALSE 4.696 1.9860 0.362586 0.8818 0.3470 2.2522 1.044925 2.431e-02 2.961e-01 TRUE 8 342.49 NA TRUE
Parabacteroides.Otu0538 3.0311 -0.638548 0.6178 -1.033630 3.013e-01 0.5033052 3.0311 2.128e+02 FALSE 14.500 11 22.823 15.000 10 FALSE 15.000 2.9314 -0.638548 1.5514 0.6178 1.8896 -1.033630 5.882e-02 3.013e-01 TRUE 12 180.03 NA TRUE
Erysipelotrichaceae_incertae_sedis.Otu0818 22.6448 -0.272972 0.2672 -1.021778 3.069e-01 0.5033052 22.6448 2.522e+03 FALSE 2.771 9 8.415 2.844 9 FALSE 2.844 5.0832 -0.272972 0.6733 0.2672 7.5497 -1.021778 4.363e-14 3.069e-01 TRUE 10 509.25 NA TRUE
Bacteroides.Otu1669 10.6606 -0.370628 0.3641 -1.018065 3.086e-01 0.5033052 10.6606 3.385e+02 FALSE 5.110 14 11.770 5.261 13 FALSE 5.261 4.2027 -0.370628 0.9169 0.3641 4.5836 -1.018065 4.570e-06 3.086e-01 TRUE 12 374.04 NA TRUE
Lachnospiraceae.Otu0220 20.8981 0.319503 0.3143 1.016472 3.094e-01 0.5033052 20.8981 1.330e+03 FALSE 3.868 13 8.073 3.950 8 FALSE 3.950 3.6209 0.319503 0.7945 0.3143 4.5572 1.016472 5.183e-06 3.094e-01 TRUE 11 474.41 NA FALSE
Clostridiales.Otu1597 0.5973 -1.310873 1.2989 -1.009228 3.129e-01 0.5033052 0.5973 1.121e+01 FALSE 67.000 9 29.241 67.000 10 FALSE 67.000 1.7559 -1.310873 3.2651 1.2989 0.5378 -1.009228 5.907e-01 3.129e-01 TRUE 11 46.49 NA TRUE
Lachnospiraceae.Otu0790 15.1499 -0.297415 0.2983 -0.996906 3.188e-01 0.5055421 15.1499 5.939e+02 FALSE 3.430 11 9.276 3.531 11 FALSE 3.531 4.5498 -0.297415 0.7518 0.2983 6.0515 -0.996906 1.435e-09 3.188e-01 TRUE 9 448.44 NA FALSE
Clostridium_XI.Otu1804 70.7088 0.266479 0.2728 0.976792 3.287e-01 0.5138398 70.7088 2.759e+04 FALSE 2.947 12 7.957 3.008 12 FALSE 3.008 5.5062 0.266479 0.6880 0.2728 8.0031 0.976792 1.213e-15 3.287e-01 TRUE 9 641.93 NA TRUE
Bacteroides.Otu0763 9.9980 -0.247173 0.2617 -0.944608 3.449e-01 0.5316577 9.9980 1.862e+02 FALSE 2.525 14 12.428 2.654 10 FALSE 2.654 3.8684 -0.247173 0.6603 0.2617 5.8587 -0.944608 4.664e-09 3.449e-01 TRUE 9 426.76 NA FALSE
Bacteroides.Otu2104 49.1926 0.267883 0.3188 0.840328 4.007e-01 0.5984206 49.1926 9.649e+03 FALSE 4.023 10 8.940 4.106 8 FALSE 4.106 4.9862 0.267883 0.8040 0.3188 6.2017 0.840328 5.586e-10 4.007e-01 TRUE 17 570.33 NA FALSE
Clostridium_XlVa.Otu1856 7.2399 -0.193598 0.2321 -0.834050 4.043e-01 0.5984206 7.2399 1.574e+02 FALSE 1.898 12 16.629 2.014 10 FALSE 2.014 3.2848 -0.193598 0.5873 0.2321 5.5930 -0.834050 2.231e-08 4.043e-01 TRUE 7 398.26 NA TRUE
Lachnospiraceae.Otu1734 17.8483 0.215959 0.2590 0.833898 4.043e-01 0.5984206 17.8483 1.434e+03 FALSE 2.575 13 8.396 2.651 9 FALSE 2.651 3.6540 0.215959 0.6556 0.2590 5.5733 0.833898 2.500e-08 4.043e-01 TRUE 9 489.99 NA FALSE
Bacteroides.Otu2383 11.6377 -0.305432 0.3920 -0.779081 4.359e-01 0.6366905 11.6377 9.736e+02 FALSE 6.011 10 11.001 6.136 10 FALSE 6.136 4.1985 -0.305432 0.9878 0.3920 4.2505 -0.779081 2.133e-05 4.359e-01 TRUE 15 358.73 NA TRUE
Bacteroides.Otu0399 3.5384 -0.319019 0.4516 -0.706430 4.799e-01 0.6863502 3.5384 7.192e+01 FALSE 7.510 9 20.897 7.914 7 FALSE 7.914 2.5089 -0.319019 1.1382 0.4516 2.2042 -0.706430 2.751e-02 4.799e-01 TRUE 11 238.50 NA TRUE
Sutterella.Otu0171 15.4575 0.554454 0.7891 0.702608 4.823e-01 0.6863502 15.4575 2.005e+03 FALSE 27.293 9 9.150 25.229 9 FALSE 25.229 2.6219 0.554454 1.9897 0.7891 1.3177 0.702608 1.876e-01 4.823e-01 TRUE 57 206.28 NA TRUE
Parabacteroides.Otu1655 1.2537 -0.448335 0.6484 -0.691433 4.893e-01 0.6874880 1.2537 1.722e+01 FALSE 14.801 10 27.850 15.874 7 FALSE 15.874 0.9526 -0.448335 1.6312 0.6484 0.5840 -0.691433 5.592e-01 4.893e-01 TRUE 11 130.33 NA TRUE
Lactobacillus.Otu1332 0.5264 -0.474225 0.8075 -0.587270 5.570e-01 0.7701997 0.5264 4.017e+00 FALSE 24.109 9 30.053 24.982 9 FALSE 24.982 0.4113 -0.474225 2.0313 0.8075 0.2025 -0.587270 8.395e-01 5.570e-01 TRUE 6 100.50 NA FALSE
Bacteroides.Otu0006 86.7512 -0.173471 0.2992 -0.579818 5.620e-01 0.7701997 86.7512 1.501e+04 FALSE 3.555 10 7.934 3.627 8 FALSE 3.627 6.8189 -0.173471 0.7537 0.2992 9.0470 -0.579818 1.470e-19 5.620e-01 TRUE 12 662.35 NA FALSE
Lachnospiracea_incertae_sedis.Otu2746 5.1181 -0.213138 0.4033 -0.528441 5.972e-01 0.7993501 5.1181 2.421e+02 FALSE 6.072 11 18.869 6.361 11 FALSE 6.361 2.8218 -0.213138 1.0179 0.4033 2.7722 -0.528441 5.567e-03 5.972e-01 TRUE 12 282.16 NA TRUE
Bacteroides.Otu2534 2.9594 -0.455557 0.8633 -0.527693 5.977e-01 0.7993501 2.9594 1.308e+02 FALSE 30.762 7 23.111 29.824 7 FALSE 29.824 2.5018 -0.455557 2.1733 0.8633 1.1512 -0.527693 2.497e-01 5.977e-01 TRUE 8 128.03 NA TRUE
Bacteroides.Otu0752 8.9932 -0.147656 0.2902 -0.508780 6.109e-01 0.8072692 8.9932 1.771e+02 FALSE 3.127 11 13.708 3.282 11 FALSE 3.282 3.5028 -0.147656 0.7332 0.2902 4.7776 -0.508780 1.774e-06 6.109e-01 TRUE 9 402.08 NA FALSE
Bacteroides.Otu2765 89.2852 0.146490 0.3088 0.474412 6.352e-01 0.8269906 89.2852 2.084e+04 FALSE 3.800 11 7.945 3.864 9 FALSE 3.864 6.1411 0.146490 0.7782 0.3088 7.8914 0.474412 2.987e-15 6.352e-01 TRUE 18 648.70 NA FALSE
Bacteroides.Otu1883 0.2152 -0.327962 0.7031 -0.466439 6.409e-01 0.8269906 0.2152 6.666e-01 FALSE 15.311 9 36.362 18.204 6 FALSE 18.204 -1.0421 -0.327962 1.7692 0.7031 -0.5890 -0.466439 5.558e-01 6.409e-01 TRUE 10 68.92 NA TRUE
Blautia.Otu2475 62.9272 0.099341 0.2229 0.445641 6.559e-01 0.8269906 62.9272 9.729e+03 FALSE 1.942 12 8.090 2.000 12 FALSE 2.000 5.7485 0.099341 0.5623 0.2229 10.2226 0.445641 1.571e-24 6.559e-01 TRUE 6 671.30 NA FALSE
Bacteroides.Otu2065 47.4786 0.370944 0.8343 0.444613 6.566e-01 0.8269906 47.4786 2.879e+04 FALSE 30.572 12 9.231 28.289 8 FALSE 28.289 4.6625 0.370944 2.1018 0.8343 2.2183 0.444613 2.653e-02 6.566e-01 TRUE 100 236.73 NA TRUE
Lachnospiraceae.Otu2599 21.4188 0.104801 0.2407 0.435342 6.633e-01 0.8269906 21.4188 1.120e+03 FALSE 2.228 11 8.114 2.295 10 FALSE 2.295 4.1739 0.104801 0.6087 0.2407 6.8566 0.435342 7.054e-12 6.633e-01 TRUE 7 522.60 NA FALSE
Blautia.Otu0591 11.1013 0.110378 0.2595 0.425417 6.705e-01 0.8269906 11.1013 5.596e+02 FALSE 2.511 12 11.396 2.619 9 FALSE 2.619 3.2143 0.110378 0.6578 0.2595 4.8862 0.425417 1.028e-06 6.705e-01 TRUE 7 436.65 NA FALSE
Bacteroides.Otu1411 5.9662 0.153814 0.3917 0.392713 6.945e-01 0.8361739 5.9662 1.917e+02 FALSE 5.751 11 18.182 6.019 11 FALSE 6.019 2.2436 0.153814 0.9923 0.3917 2.2611 0.392713 2.375e-02 6.945e-01 TRUE 14 308.19 NA TRUE
Bacteroides.Otu0786 61.4087 0.212022 0.5464 0.388015 6.980e-01 0.8361739 61.4087 3.773e+04 FALSE 12.316 11 8.134 12.126 11 FALSE 12.126 5.4512 0.212022 1.3767 0.5464 3.9596 0.388015 7.508e-05 6.980e-01 TRUE 65 404.38 NA TRUE
Bacteroides.Otu2069 16.8564 0.189685 0.4933 0.384540 7.006e-01 0.8361739 16.8564 2.401e+03 FALSE 9.873 12 8.658 9.818 9 FALSE 9.818 3.6382 0.189685 1.2442 0.4933 2.9242 0.384540 3.454e-03 7.006e-01 TRUE 31 329.76 NA TRUE
Bacteroides.Otu2343 42.0294 0.191298 0.5119 0.373680 7.086e-01 0.8368014 42.0294 1.442e+04 FALSE 10.634 14 10.572 10.630 5 FALSE 10.630 4.9521 0.191298 1.2900 0.5119 3.8387 0.373680 1.237e-04 7.086e-01 TRUE 54 391.66 NA TRUE
Faecalibacterium.Otu0751 44.5838 -0.070555 0.2198 -0.321009 7.482e-01 0.8742165 44.5838 4.619e+03 FALSE 1.863 12 9.871 1.936 10 FALSE 1.936 5.6349 -0.070555 0.5544 0.2198 10.1642 -0.321009 2.864e-24 7.482e-01 TRUE 6 630.00 NA FALSE
Bacteroides.Otu2216 8.7397 0.210756 0.8013 0.263033 7.925e-01 0.9055634 8.7397 1.481e+03 FALSE 27.369 10 14.098 25.960 10 FALSE 25.960 2.6202 0.210756 2.0203 0.8013 1.2969 0.263033 1.947e-01 7.925e-01 TRUE 26 180.16 NA TRUE
Bacteroides.Otu1976 4.7104 0.261721 1.0196 0.256700 7.974e-01 0.9055634 4.7104 2.990e+02 FALSE 47.035 7 19.171 41.990 8 FALSE 41.990 1.6112 0.261721 2.5715 1.0196 0.6266 0.256700 5.309e-01 7.974e-01 TRUE 19 132.57 NA TRUE
Bacteroides.Otu0312 0.3573 -0.165224 0.6505 -0.253986 7.995e-01 0.9055634 0.3573 1.186e+00 FALSE 13.598 9 32.948 15.543 9 FALSE 15.543 -0.7638 -0.165224 1.6399 0.6505 -0.4658 -0.253986 6.414e-01 7.995e-01 TRUE 9 91.28 NA TRUE
Faecalibacterium.Otu0067 172.4012 0.049423 0.2123 0.232768 8.159e-01 0.9060835 172.4012 5.869e+04 FALSE 1.770 12 8.093 1.827 12 FALSE 1.827 7.3172 0.049423 0.5351 0.2123 13.6752 0.232768 1.429e-42 8.159e-01 TRUE 6 810.51 NA FALSE
Bacteroides.Otu0883 1.6394 0.165709 0.7133 0.232317 8.163e-01 0.9060835 1.6394 2.907e+01 FALSE 19.264 8 27.342 19.947 6 FALSE 19.947 0.3800 0.165709 1.8067 0.7133 0.2103 0.232317 8.334e-01 8.163e-01 TRUE 24 139.72 NA TRUE
Parabacteroides.Otu1107 8.0975 -0.119809 0.6308 -0.189917 8.494e-01 0.9334708 8.0975 4.723e+02 FALSE 16.082 8 15.218 16.029 8 FALSE 16.029 3.2791 -0.119809 1.5902 0.6308 2.0621 -0.189917 3.920e-02 8.494e-01 TRUE 23 235.64 NA TRUE
Bacteroides.Otu0775 10.8844 -0.055285 0.3649 -0.151514 8.796e-01 0.9484139 10.8844 4.799e+02 FALSE 5.155 11 11.574 5.297 11 FALSE 5.297 3.5727 -0.055285 0.9211 0.3649 3.8787 -0.151514 1.050e-04 8.796e-01 TRUE 14 374.92 NA TRUE
Megamonas.Otu2657 5.9719 0.188744 1.2854 0.146831 8.833e-01 0.9484139 5.9719 1.219e+03 FALSE 67.000 9 18.177 67.000 9 FALSE 67.000 2.1373 0.188744 3.2395 1.2854 0.6598 0.146831 5.094e-01 8.833e-01 TRUE 9 70.26 NA TRUE
Lachnospiracea_incertae_sedis.Otu1990 3.8519 0.059533 0.4250 0.140071 8.886e-01 0.9484139 3.8519 9.641e+01 FALSE 6.652 9 20.170 7.013 8 FALSE 7.013 1.8261 0.059533 1.0772 0.4250 1.6952 0.140071 9.003e-02 8.886e-01 TRUE 10 259.54 NA TRUE
Bacteroides.Otu2038 215.2013 0.044933 0.3560 0.126215 8.996e-01 0.9509652 215.2013 2.629e+05 FALSE 5.100 12 8.039 5.150 10 FALSE 5.150 7.6477 0.044933 0.8968 0.3560 8.5281 0.126215 1.487e-17 8.996e-01 TRUE 27 692.20 NA FALSE
Bacteroides.Otu2375 28.9078 -0.031249 0.2935 -0.106470 9.152e-01 0.9583798 28.9078 1.901e+03 FALSE 3.346 11 11.740 3.459 10 FALSE 3.459 4.9293 -0.031249 0.7403 0.2935 6.6588 -0.106470 2.761e-11 9.152e-01 TRUE 11 532.96 NA FALSE
Bacteroides.Otu2431 122.8406 -0.025774 0.2993 -0.086130 9.314e-01 0.9661807 122.8406 4.272e+04 FALSE 3.567 12 8.093 3.633 10 FALSE 3.633 6.9987 -0.025774 0.7539 0.2993 9.2828 -0.086130 1.651e-20 9.314e-01 TRUE 13 698.28 NA FALSE
Bacteroides.Otu0200 10.2709 0.020221 0.6180 0.032722 9.739e-01 0.9859926 10.2709 1.006e+03 FALSE 15.617 10 12.141 15.407 8 FALSE 15.407 3.3024 0.020221 1.5581 0.6180 2.1196 0.032722 3.404e-02 9.739e-01 TRUE 15 230.90 NA TRUE
Bacteroides.Otu2437 29.1144 -0.014843 0.5101 -0.029101 9.768e-01 0.9859926 29.1144 4.785e+03 FALSE 10.485 11 11.841 10.540 9 FALSE 10.540 4.8977 -0.014843 1.2853 0.5101 3.8106 -0.029101 1.386e-04 9.768e-01 TRUE 36 379.16 NA TRUE
Escherichia_Shigella.Otu2393 8.3285 0.013216 0.4606 0.028693 9.771e-01 0.9859926 8.3285 5.753e+02 FALSE 8.276 11 14.800 8.472 11 FALSE 8.472 3.0143 0.013216 1.1628 0.4606 2.5924 0.028693 9.531e-03 9.771e-01 TRUE 12 286.84 NA TRUE
Parabacteroides.Otu1378 29.5767 0.003782 0.5580 0.006779 9.946e-01 0.9945913 29.5767 5.842e+03 FALSE 12.648 10 12.053 12.622 7 FALSE 12.622 4.8773 0.003782 1.4059 0.5580 3.4693 0.006779 5.219e-04 9.946e-01 TRUE 60 352.10 NA TRUE
Bacteria.Otu0435 0.0000 0.000000 0.0000 0.000000 1.000e+00 NA 0.0000 0.000e+00 TRUE 67.000 2 13.087 67.000 8 FALSE 67.000 NA NA NA NA NA NA NA NA NA NA NA NA TRUE

(1.6.1.4.2.2.1) Figure 1028. Clustered heatmap of normalized abundance values. Number of cluster splits is determined automatically with method fpc::pamk. Image file: plots/323ed79c0a.svg.

(1.6.1.4.2.2.1) G-test of independence between automatic cluster splits and attribute 'visit'. Number of cluster splits is determined automatically with method fpc::pamk.

Log likelihood ratio (G-test) test of independence with Williams' correction: m_a$attr[, main.meta.var] and split
Test statistic X-squared df P value
3.559 3 0.3131

Wrote counts and metadata for raw counts Data used for heatmap with added row cluster splits to files data/1.6.1.4.2.2.1-323717f952csamples.raw.htmap.count.tsv,data/1.6.1.4.2.2.1-323717f952csamples.raw.htmap.attr.tsv

(1.6.1.4.2.3) Default transformations for further data analysis

Specific methods can override these and use their own normalization.

Count normalization method for data analysis (unless modified by specific methods) : [ drop.features:List of 1, ..$ :"other", method.args :List of 1, ..$ theta:1, method :"norm.ihs.prop"]

Wrote counts and metadata for raw counts Normalized after default transformations to files data/1.6.1.4.2.3-32319dd7d29samples.raw.16s.l.otu.count.tsv,data/1.6.1.4.2.3-32319dd7d29samples.raw.16s.l.otu.attr.tsv

(1.6.1.4.3) Stability selection analysis for response ( visit )

(1.6.1.4.3) Summary of response variable visit.

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  1.000   1.000   2.000   2.254   3.000   4.000 

Hofner B, Hothorn T (2017). stabs: Stability Selection with Error Control. R package version 0.6-3, <URL: https://CRAN.R-project.org/package=stabs>.

Hofner B, Boccuto L, Göker M (2015). “Controlling false discoveries in high-dimensional situations: Boosting with stability selection.” BMC Bioinformatics, 16, 144. <URL: http://dx.doi.org/10.1186/s12859-015-0575-3>.

Thomas J, Mayr A, Bischl B, Schmid M, Smith A, Hofner B (2017). “Gradient boosting for distributional regression - faster tuning and improved variable selection via noncyclical updates.” Statistics and Computing. doi: 10.1007/s11222-017-9754-6 (URL: http://doi.org/10.1007/s11222-017-9754-6), Online First.

This multivariate feature selection method implements stability selection procedure by Meinshausen and Buehlmann (2010) and the improved error bounds by Shah and Samworth (2013). The features (e.g. taxonomic features) are ranked according to their probability to be selected by models built on multiple random subsamples of the input dataset.

Base selection method parameters that were chosen based on cross-validation are: [ alpha:0.3]

All base selection method parameters are: [ family :"gaussian", standardize:TRUE, alpha :0.3]

Stability selection method parameters are: [ PFER :0.05, sampling.type:"SS", assumption :"r-concave", B :400, q :8]

(1.6.1.4.3) Table 446. Selection probability for the variables. Probability cutoff=0.845 corresponds to per family error rate PFER=0.0498. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.6.1.4.3-3234ec4c761.1.6.1.4.3.a.name.ta.csv

  Prob(selection)
Roseburia.Otu2084 0.88750
Lachnospiraceae.Otu2076 0.55000
Lachnospiracea_incertae_sedis.Otu0778 0.49125
Roseburia.Otu1051 0.46750
Roseburia.Otu2637 0.35375
Alistipes.Otu1466 0.22750
Lachnospiraceae.Otu1734 0.22375
Bacteroides.Otu0775 0.22125
Haemophilus.Otu1497 0.21000
Bacteroides.Otu0863 0.19500
Bacteroides.Otu2460 0.18875
Bacteroides.Otu2654 0.17125
Lachnospiraceae.Otu2599 0.15500
Clostridium_XI.Otu2681 0.15250
Bacteroides.Otu2437 0.13500
Parabacteroides.Otu1655 0.12125
Prevotella.Otu0634 0.09375
Escherichia_Shigella.Otu2393 0.08625
Lachnospiraceae.Otu0898 0.08375
Parabacteroides.Otu1378 0.08375
Clostridiaceae_1.Otu1955 0.07875
Bacteroides.Otu1411 0.07875
Faecalibacterium.Otu0067 0.07750
Bacteroides.Otu1883 0.07750
Klebsiella.Otu1452 0.07250
Sutterella.Otu0171 0.07125
Lachnospiraceae.Otu2222 0.07000
Bacteroides.Otu1669 0.06875
Lachnospiraceae.Otu0220 0.06125
Roseburia.Otu2728 0.06125
Phascolarctobacterium.Otu1814 0.06000
Prevotella.Otu1633 0.05875
Bacteroides.Otu2216 0.05625
Bacteroides.Otu2431 0.05500
Bacteroides.Otu2343 0.05500
Bacteroides.Otu0848 0.05125
Parabacteroides.Otu1107 0.05125
Lachnospiraceae.Otu0491 0.05125
Bacteroides.Otu1976 0.05000
Bacteroides.Otu2065 0.04625
Bacteroides.Otu1201 0.04375
Lachnospiracea_incertae_sedis.Otu0113 0.03875
Bacteroides.Otu1352 0.03875
Bacteroides.Otu0883 0.03750
Lachnospiraceae.Otu2512 0.03625
Bacteroides.Otu2069 0.03625
Gemmiger.Otu0907 0.03625
Prevotella.Otu0882 0.03375
Lachnospiraceae.Otu0033 0.03125
Bacteroides.Otu0752 0.03125
Clostridium_XlVa.Otu1856 0.03000
Alistipes.Otu2508 0.02875
Bacteroides.Otu0399 0.02875
Bacteroides.Otu2375 0.02750
Bacteroides.Otu0661 0.02500
Bacteroides.Otu0312 0.02500
Faecalibacterium.Otu0751 0.02375
Bacteroides.Otu0877 0.02375
Bacteroides.Otu2120 0.02375
Bacteroides.Otu2523 0.02375
Bacteroides.Otu2038 0.02125
Bacteroides.Otu0786 0.02125
Parabacteroides.Otu0538 0.02125
Bacteroides.Otu2520 0.02000
Bacteroides.Otu2765 0.02000
Blautia.Otu2475 0.02000
Dorea.Otu1142 0.02000
Lachnospiracea_incertae_sedis.Otu1990 0.02000
Bacteroides.Otu0001 0.01875
Clostridium_XlVa.Otu0236 0.01750
Lachnospiracea_incertae_sedis.Otu2746 0.01750
Bacteroides.Otu2625 0.01625
Bacteroides.Otu0006 0.01625
Lachnospiraceae.Otu0790 0.01625
Bacteroides.Otu2104 0.01500
Prevotella.Otu2602 0.01500
Bacteroides.Otu0069 0.01375
Erysipelotrichaceae_incertae_sedis.Otu0818 0.01375
Akkermansia.Otu1935 0.01375
Bacteroides.Otu2416 0.01375
Bacteroides.Otu2383 0.01125
Bacteroides.Otu0480 0.01000
Sutterella.Otu1997 0.01000
Turicibacter.Otu0468 0.00875
Prevotella.Otu2501 0.00875
Prevotella.Otu2327 0.00875
Clostridium_XI.Otu1804 0.00750
Bacteroides.Otu2534 0.00750
Bacteroides.Otu0763 0.00750
Clostridiales.Otu0562 0.00625
Blautia.Otu0620 0.00625
Bacteroides.Otu0929 0.00500
Bacteroidales.Otu0696 0.00500
Clostridiales.Otu1597 0.00500
Barnesiella.Otu2015 0.00500
Prevotella.Otu2227 0.00500
Veillonella.Otu0362 0.00375
Prevotella.Otu1994 0.00375
Blautia.Otu0591 0.00375
Megamonas.Otu2657 0.00250
Prevotella.Otu1319 0.00250
Bacteroides.Otu0200 0.00250
Prevotella.Otu1987 0.00125
Lactobacillus.Otu1332 0.00125
Parabacteroides.Otu1736 0.00000
Enterococcus.Otu1019 0.00000
Lachnospiracea_incertae_sedis.Otu0651 0.00000
Prevotella.Otu1803 0.00000
Prevotella.Otu0738 0.00000
Prevotella.Otu0773 0.00000
Bacteria.Otu0435 0.00000
Burkholderiales.Otu0023 0.00000

(1.6.1.4.3) Figure 1029. Selection probability for the top ranked variables. Probability cutoff=0.845 corresponds to per family error rate PFER=0.0498 (vertical line). Image file: plots/323578100fc.svg.

(1.6.1.4.4) PermANOVA (adonis) analysis of normalized counts

Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, Minchin PR, O'Hara RB, Simpson GL, Solymos P, Stevens MHH, Szoecs E, Wagner H (2018). vegan: Community Ecology Package. R package version 2.5-2, <URL: https://CRAN.R-project.org/package=vegan>.

Non-parametric multivariate test for association between normalized counts and meta-data variables. Dissimilarity index is euclidean.

(1.6.1.4.4) Association with visit paired by subject with formula count~visit with strata = SubjectID.

Permutation test for adonis under reduced model
Terms added sequentially (first to last)
Blocks:  m_a$attr[, strata] 
Permutation: free
Number of permutations: 4000

adonis2(formula = as.formula(formula_str), data = m_a$attr, permutations = perm, method = dist.metr)
         Df SumOfSqs      R2      F Pr(>F)
visit     1    0.088 0.01223 0.8045 0.7248
Residual 65    7.110 0.98777              
Total    66    7.198 1.00000              

(1.6.1.4.4) Association with visit paired by subject Adonis summary.

Permutation test for adonis under reduced model
  Df SumOfSqs R2 F Pr(>F)
visit 1 0.088 0.0122 0.8045 0.7248
Residual 65 7.11 0.9878 NA NA
Total 66 7.198 1 NA NA

Count normalization method for abundance plots : [ drop.features:List of 1, ..$ :"other", method.args : list(), method :"norm.prop"]

(1.6.1.4.5) Plots of Abundance.

Subreport

(1.6.1.4.5) Figure 1056. Clustered heatmap of normalized abundance values. Number of cluster splits is determined automatically with method fpc::pamk. Image file: plots/3231e6a0de1.svg.

(1.6.1.4.5) G-test of independence between automatic cluster splits and attribute 'visit'. Number of cluster splits is determined automatically with method fpc::pamk.

Log likelihood ratio (G-test) test of independence with Williams' correction: m_a$attr[, main.meta.var] and split
Test statistic X-squared df P value
24.95 24 0.4087

person) (????). morpheus: Interactive heat maps using 'morpheus.js' and 'htmlwidgets'. R package version 0.1.1.1, <URL: https://github.com/cmap/morpheus.R>.

(1.6.1.4.5) Widget 462. Dynamic Morpheus heatmap of normalized abundance values. It is available here through the link only because it can take a while to render for large datasets. This is very customizable. What you will see initially is just a default starting configuration. Explore its menus. Click to see HTML widget file in full window: ./1.6.1.4.5-32350c78094Dynamic.Morpheus.hea.html

Wrote counts and metadata for raw counts Data used for heatmap with added row cluster splits (clustering by abundance profile) to files data/1.6.1.4.5-32331812ce8samples.raw.htmap.count.tsv,data/1.6.1.4.5-32331812ce8samples.raw.htmap.attr.tsv

(1.6.1.4.5) Figure 1057. Clustered heatmap of diversity and normalized abundance values. Number of cluster splits is determined automatically with method fpc::pamk. Image file: plots/32379f9d705.svg.

(1.6.1.4.5) G-test of independence between automatic cluster splits and attribute 'visit'. Number of cluster splits is determined automatically with method fpc::pamk.

Log likelihood ratio (G-test) test of independence with Williams' correction: m_a$attr[, main.meta.var] and split
Test statistic X-squared df P value
1.485 3 0.6858

Wrote counts and metadata for raw counts Data used for heatmap with added row cluster splits (clustering by Renyi diversity indices) to files data/1.6.1.4.5-3235f3c374asamples.raw.htmap.count.tsv,data/1.6.1.4.5-3235f3c374asamples.raw.htmap.attr.tsv

(1.6.1.4.6) Ordinations,

Subreport

(1.6.1.4.7) Network Analysis Feature correlation with overlaid differential abundance results

Subreport

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